Retrotransposons and their recognition of pol II promoters:: A comprehensive survey of the transposable elements from the complete genome sequence of Schizosaccharomyces pombe
Retrotransposons and their recognition of pol II promoters:: A comprehensive survey of the transposable elements from the complete genome sequence of Schizosaccharomyces pombe
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DOI：
10.1101/gr.1191603
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发表时间：
2003-09-01
期刊：
影响因子：
7
通讯作者：
Levin, HL
中科院分区：
文献类型：
--
作者：
Bowen, NJ;Jordan, IK;Levin, HL
粟酒裂殖酵母基因组的完整DNA序列提供了研究转座因子（TE）的整个互补序列、它们与特定序列的关联、它们的染色体分布以及它们的进化的机会。通过同源性序列鉴定，我们发现测序的S。pombe只含有一个全长转座子家族。这个家族，Tf2，由13个全长拷贝的长末端重复序列（LTR）反转录转座子组成。我们发现先前存在的转座子的LTR-LTR重组导致了大量的单独LTR。其中包括35个Tf2的单独LTR，以及139个来自其他Tf家族的单独LTR。系统发育分析表明，Tf 1和Tf 2是基因组中最近的活性元件。单独的LTR也充当Tf反转录转座子先前插入事件的足迹。对186个基因组插入事件的分析揭示了与RNA聚合酶II启动子的密切关联。这些插入位于基因的启动子近端区域，蛋白质编码区上游100至400个核苷酸。Tf插入与pol II启动子的关联与先前观察到的Tf 1整合的偏好非常相似。我们发现，最近活跃的Tf元素是不存在的着丝粒和近着丝粒区的基因组含有串联tRNA基因簇。此外，我们的分析表明，染色体III的插入事件的密度是其他两条染色体的两倍。最后，我们描述了一个新的重复序列，wtf，这也是优先位于油染色体III，往往位于附近的Tf元件的独奏LTR。
The complete DNA sequence of the genome of Schizosaccharomyces pombe provides the opportunity to investigate the entire complement of transposable elements (TEs), their association with specific sequences, their chromosomal distribution, and their evolution. Using homology-based sequence identification, we found that the sequenced strain of S. pombe contained only one family of full-length transposons. This family, Tf2, consisted of 13 full-length copies of a long terminal repeat (LTR) retrotransposon. We found that LTR-LTR recombination of previously existing transposons had resulted in extensive populations of solo LTRs. These included 35 solo LTRs of Tf2, as well as 139 solo LTRs from other Tf families. Phylogenetic analysis of solo Tf LTRs reveals that Tf1 and Tf2 were the most recently active elements within the genome. The solo LTRs also served as footprints for previous insertion events by the Tf retrotransposons. Analysis of 186 genomic insertion events revealed a close association with RNA polymerase II promoters. These insertions Clustered in the promoter-proximal regions of genes, upstream of protein coding regions by 100 to 400 nucleotides. The association of Tf insertions with pol II promoters was very similar to the preference previously observed for Tf1 integration. We found that the recently active Tf elements were absent from centromeres and pericentromeric regions of the genome containing tandem tRNA gene clusters. In addition, Our analysis revealed that chromosome III has twice the density of insertion events compared to the other two chromosomes. Finally we describe a novel repetitive sequence, wtf, which was also preferentially located oil chromosome III, and was often located near solo LTRs of Tf elements.